gs_get_singlecell_expression_by_gate error

[mikejiang]

I’m currently working with flowWorkspace and I’m trying to use gs_get_singlecell_expression_by_gate

nodes1<- c("mono", "gran", "B", "NK","CD4+", "CD8+", "CD45+") gs_get_singlecell_expression_by_gate(gs[1],nodes1)

Error in .cpp_getSingleCellExpressionByGate(x@pointer, sample, markers_pops, : NA not found!

Margaret Cui

[mikejiang]

It is because gs_get_singlecell_expression_by_gate tries to retrieve the markers that are associated with the gates. And CD45+ gate is defined on SSC-A, which doesn't have marker.

gh_pop_get_gate(gs[[1]], "CD45+")
Polygonal gate 'CD45+' with 5 vertices in dimensions Alexa Fluor 405-A and SSC-A

This why it reports NA error.

[mlcui]

Does this mean there is another method to retrieve SSC-A and FSC-A data? It would be useful to help differentiate cell populations with size and granularity on a tSNE plot.

[gfinak]

A workaround is to put a markername in the SSC-A channel.

[mikejiang]

We can probably do that automatically within the gs_get_singlecell_expression_by_gate call

[mikejiang]

Here is the result after the patch,

 testData<-gs_get_singlecell_expression_by_gate(gs[1],nodes1)
.
> head(testData[[1]])
          CD14    CD11b     CD16     CD20 CD4 CD8     CD45     SSC-A
[1,] 0.0000000 0.000000 0.000000 0.000000   0   0 3.984200  12014.69
[2,] 0.0000000 0.000000 0.000000 0.000000   0   0 3.801033  34185.41
[3,] 0.0000000 0.000000 1.039903 2.586087   0   0 3.737607  71270.02

[mlcui]

Thanks Mike!